[2024-01-24 15:02:24,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference
[2024-01-24 15:02:26,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,433] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,433] [INFO] Running command: gunzip -c /var/lib/cwl/stge39b1134-1b99-4cfb-a426-bc302877029b/GCF_006265115.1_ASM626511v1_genomic.fna.gz | prodigal -d GCF_006265115.1_ASM626511v1_genomic.fna/cds.fna -a GCF_006265115.1_ASM626511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:36,222] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:36,223] [INFO] Task started: HMMsearch
[2024-01-24 15:02:36,223] [INFO] Running command: hmmsearch --tblout GCF_006265115.1_ASM626511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/reference_markers.hmm GCF_006265115.1_ASM626511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:36,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:36,547] [INFO] Found 6/6 markers.
[2024-01-24 15:02:36,581] [INFO] Query marker FASTA was written to GCF_006265115.1_ASM626511v1_genomic.fna/markers.fasta
[2024-01-24 15:02:36,581] [INFO] Task started: Blastn
[2024-01-24 15:02:36,582] [INFO] Running command: blastn -query GCF_006265115.1_ASM626511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/reference_markers.fasta -out GCF_006265115.1_ASM626511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:37,699] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:37,703] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:37,704] [INFO] Target genome list was writen to GCF_006265115.1_ASM626511v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:37,739] [INFO] Task started: fastANI
[2024-01-24 15:02:37,739] [INFO] Running command: fastANI --query /var/lib/cwl/stge39b1134-1b99-4cfb-a426-bc302877029b/GCF_006265115.1_ASM626511v1_genomic.fna.gz --refList GCF_006265115.1_ASM626511v1_genomic.fna/target_genomes.txt --output GCF_006265115.1_ASM626511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:49,688] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:49,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:49,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:49,704] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:49,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:49,705] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	100.0	1101	1102	95	conclusive
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	86.7557	771	1102	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	86.3595	701	1102	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	85.6998	711	1102	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	84.7098	761	1102	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	84.4674	711	1102	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	83.7012	709	1102	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	83.6091	723	1102	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.4294	543	1102	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.3599	529	1102	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	79.9947	511	1102	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	79.79	533	1102	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.782	564	1102	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	79.4372	302	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:49,706] [INFO] DFAST Taxonomy check result was written to GCF_006265115.1_ASM626511v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:49,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:49,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:49,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/checkm_data
[2024-01-24 15:02:49,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:49,748] [INFO] Task started: CheckM
[2024-01-24 15:02:49,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006265115.1_ASM626511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006265115.1_ASM626511v1_genomic.fna/checkm_input GCF_006265115.1_ASM626511v1_genomic.fna/checkm_result
[2024-01-24 15:03:28,003] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:28,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:28,019] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:28,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:28,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006265115.1_ASM626511v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:28,021] [INFO] Task started: Blastn
[2024-01-24 15:03:28,021] [INFO] Running command: blastn -query GCF_006265115.1_ASM626511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c9f65ba-44bf-4868-87c4-ae8a897f0f31/dqc_reference/reference_markers_gtdb.fasta -out GCF_006265115.1_ASM626511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:30,334] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:30,337] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:30,337] [INFO] Target genome list was writen to GCF_006265115.1_ASM626511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:30,347] [INFO] Task started: fastANI
[2024-01-24 15:03:30,347] [INFO] Running command: fastANI --query /var/lib/cwl/stge39b1134-1b99-4cfb-a426-bc302877029b/GCF_006265115.1_ASM626511v1_genomic.fna.gz --refList GCF_006265115.1_ASM626511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006265115.1_ASM626511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:40,206] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:40,217] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:40,217] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_006265115.1	s__Arenimonas terrae	100.0	1101	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007993735.1	s__Arenimonas daejeonensis	88.545	838	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	86.7713	770	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	86.3942	699	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	85.6877	712	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	85.5923	739	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	85.3985	554	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCA_003241895.1	s__Arenimonas sp003241895	84.8995	735	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	84.6711	764	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	83.6051	723	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_006337105.1	s__Thermomonas sp006337105	80.4185	544	1102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:40,219] [INFO] GTDB search result was written to GCF_006265115.1_ASM626511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:40,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:40,226] [INFO] DFAST_QC result json was written to GCF_006265115.1_ASM626511v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:40,226] [INFO] DFAST_QC completed!
[2024-01-24 15:03:40,226] [INFO] Total running time: 0h1m16s